How to contribute to Sage

Sébastien Labbé

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Sage Days 28

Orsay, France, January 17-19th 2011

GNU General Public Licence

Sage is distributed under the terms of the GNU General Public License version 2 (GPLv2) which provides four kinds of freedom:

  • Freedom to run the program
  • Freedom to access the code
  • Freedom to redistribute the program to anyone
  • Freedom to improve the software

While all users of Sage make use of the first freedom, in this talk, we will see how to appropriate the other three.

Twenty Two Easy Steps

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  1. Find a bug
  1. Build the documentation
  1. Sage trac server
  1. Update the current patch
  1. Create a ticket
  1. Export a patch
  1. Clone your Sage
  1. Verify the patch
  1. Mercurial
  1. Upload the patch
  1. Enable Mercurial queues
  1. More on Mercurial queues
  1. Create an empty patch
  1. Dowload a patch
  1. Fix the bug
  1. Edit the series file
  1. View your changes
  1. Reviewing a patch
  1. Test the changes
  1. Positive review or Needs work
  1. Run tests
  1. Do some cleaning
Are you ready?

1. Find a bug

That’s the easiest part. Choose one amongst this

made for Sage Days 28 or browse the

During this talk, instead of fixing a bug I am going to introduce one in the inverse method of a permutation.

2. Sage trac server

In Sage, modifications are tracked on a web site called Sage trac. Every bug gets assigned a number. For instance, the number #10484 refers to the bug called Chinese remainder code raises an error when called with Python ints. On the ticket, one can see that:

  • The bug was reported and solved by David Loeffler (UK) in December 2010.
  • The ticket was positively reviewed by Robert Bradshaw (USA) and Mike Hansen.
  • The solution was merged in sage-4.6.2 by Jeroen Demeyer (Belgium) on January 11th 2011.

One can also look at the solution, download it, test it, etc.

3. Create a ticket

In order to create a ticket:

  • Create an account on http://trac.sagemath.org/sage_trac/register
  • Login to your account
  • Make sure the ticket does not already exists.
  • Create ticket
  • In the description field, explain how should someone else understand and/or reproduce the bug.

I create the imaginary ticket #12345 for introducing a useless print statement in the method that computes the inverse of a permutation.

4. Clone your version of Sage

Clone Sage and create your branch (Do it right now because it might take some time)
sage -clone slabbe

This creates a new directory called sage-slabbe in the devel repository:

slabbe@pol ~/Applications/sage-4.6.1/devel $ ls -l
drwxr-xr-x  2 slabbe staff  68 14 jan 03:59 old/
lrwxr-xr-x  1 slabbe staff   9 18 jan 15:01 sage -> sage-main/
drwxr-xr-x 23 slabbe staff 782 18 jan 01:42 sage-main/
drwxr-xr-x 24 slabbe staff 816 17 jan 01:50 sage-slabbe/
lrwxr-xr-x  1 slabbe staff  11 14 jan 03:42 sagenb -> sagenb-main/
drwxr-xr-x 21 slabbe staff 714 14 jan 03:41 sagenb-main/
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Build the main branch Build my branch slabbe Print the current branch
sage -b main sage -b slabbe sage -branch

5. Mercurial

Sage uses the program Mercurial ( hg or sage -hg ) to manage all of its source code. Mercurial stores the evolution of every single file of Sage since the beginning.

Since I am too lazy to write sage -hg everytime I use Mercurial, I added the following line to my ~/.bashrc file:

alias hg='sage -hg'

I verify that it works:

slabbe@pol ~ $ hg --version
Mercurial Distributed SCM (version 1.6.4)

Copyright (C) 2005-2010 Matt Mackall <mpm@selenic.com> and others
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

5. Mercurial

hg log
Print the revision history of the specified files or the entire project.
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-main $ hg log

changeset:   15205:f24ce048fa66
tag:         tip
user:        Jeroen Demeyer
date:        Tue Jan 11 08:10:26 2011 +0100
summary:     4.6.1

...

changeset:   0:039f6310c6fe
user:        tornaria
date:        Sat Feb 11 01:13:08 2006 +0000
summary:     [project @ original sage-0.10.12]
hg update
Update the repository’s working directory to the specified changeset.

6. Enable Mercurial queues

Mercurial queues is an extension to Mercurial that allows one to easily work with collections of patches. To allow Mercurial queues, edit (or create) the file ~/.hgrc and make sure it contains the line hgext.mq = in the extensions section:

[ui]
username = Sebastien Labbe <hidden adress email>
[extensions]
hgext.mq =
color =
[alias]
qstatus = status --rev -2:.

Warning

The line hgext.mq= is an indispensable for the next steps.

7. Create an empty patch

cd to your branch:

cd Applications/sage-4.6.1/devel/sage-slabbe

Create a new empty patch:

hg qnew trac_12345-add_useless_print-sl.patch

8. Fix the bug

Find the file containing the bug

Personnally I found the file permutation.py here:

sage-4.6.1/devel/sage-slabbe/sage/combinat/permutation.py

Find the solution to the bug

Edit the source code accordingly, save and quit

9. View your changes

Now, you may use the following Mercurial commands to look at your local changes.

hg status shows changed files since last hg qnew (or hg qrefresh):

slabbe@pol ~/Applications/sage-4.6.1/devel/sage-combinat/sage/combinat $ hg status
M sage/combinat/permutation.py

hg diff shows differences since last hg qnew (or hg qrefresh)

slabbe@pol ~/Applications/sage-4.6.1/devel/sage-combinat/sage/combinat $ hg diff
diff --git a/sage/combinat/permutation.py b/sage/combinat/permutation.py
--- a/sage/combinat/permutation.py
+++ b/sage/combinat/permutation.py
@@ -1208,6 +1208,7 @@ class Permutation_class(CombinatorialObj
             sage: Permutation([2, 4, 1, 5, 3]).inverse()
             [3, 1, 5, 2, 4]
         """
+        print "YO !!!! Let's inverse some permutations !!!"
         w = range(len(self))
         for i,j in enumerate(self):
             w[j-1] = i+1

10. Test the changes

Build sage
sage -b
Verify the effects of the modification
Run sage
sage: p = Permutation([4,3,2,5,1])
sage: p.inverse()
YO !!!! Let's inverse some permutations !!!
[5, 3, 2, 1, 4]

That’s great: we are now able to modify Sage.

11. Run tests

Make sure that all examples in the source code still work
sage -t <files>
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe/sage/combinat $ sage -t permutation.py
sage -t  "devel/sage-slabbe/sage/combinat/permutation.py"
**********************************************************************
File "/Users/slabbe/Applications/sage-4.6.1/devel/sage-slabbe/sage/combinat/permutation.py", line 1206:
    sage: Permutation([3,8,5,10,9,4,6,1,7,2]).inverse()
Expected:
    [8, 10, 1, 6, 3, 7, 9, 2, 5, 4]
Got:
    YO !!!! Let's inverse some permutations !!!
    [8, 10, 1, 6, 3, 7, 9, 2, 5, 4]
----------------------------------------------------------------------
The following tests failed:
    sage -t  "devel/sage-slabbe/sage/combinat/permutation.py"
Total time for all tests: 10.4 seconds

If tests failed, one should edit files again...

12. Build the documentation

Build the documentation and make sure there are no errors or warnings:

sage -b && sage -docbuild reference html

Open the html version of documentation in your browser and make sure the documentation looks OK:

open ~/Applications/sage-4.6.1/devel/sage/doc/output/html/en/reference/sage/combinat/permutation.html

13. Update the current patch

When the bug is fixed, once we made sure every tests pass and that the documentation builds fine, then we can update the current patch with hg qrefresh to reflect the changes:

hg qrefresh

No changes are shown anymore by hg status or hg diff:

hg status
hg diff

Modifications are now in the patch. See hg qstatus or hg qdiff:

hg qstatus
hg qdiff

14. Export a patch

Add a commit message to the patch:

hg qrefresh -m "#12345: add a useless print in the inverse method of a permutation"

Export the patch with hg export:

hg export trac_12345-add_useless_print-sl.patch >
         ~/Documents/tmp/trac_12345-add_useless_print-sl.patch

The command hg export also adds informations in the patch (author name, date, ...).

Note

Personnaly, I added the following alias to my ~/.bashrc:

alias qtoptotmp='hg export `hg qtop` > ~/Documents/tmp/`hg qtop`'

15. Verify the content the patch

Here is an example of a patch exported by Mercurial for the imaginary ticket #12345. It contains information about the author, the date, the commit message we just wrote and finally the complete diff.

trac_12345-add_useless_print-sl.patch:

# HG changeset patch
# User Sebastien Labbe <hidden adress email>
# Date 1295311529 -3600
# Node ID 4a6379cf0c965e1ce309846cbcb9f864932a3b6c
# Parent  83e5e45a8935ac627c45ed14042bbebafeb1a800
#12345: add a useless print in the inverse method of a permutation

diff --git a/sage/combinat/permutation.py b/sage/combinat/permutation.py
--- a/sage/combinat/permutation.py
+++ b/sage/combinat/permutation.py
@@ -1208,6 +1208,7 @@ class Permutation_class(CombinatorialObj
             sage: Permutation([2, 4, 1, 5, 3]).inverse()
             [3, 1, 5, 2, 4]
         """
+        print "YO !!!! Let's inverse some permutations !!!"
         w = range(len(self))
         for i,j in enumerate(self):
             w[j-1] = i+1

16. Upload the patch on Sage trac

Upload the patch on Sage trac

You can mention things like “tested on sage-4.6.1” in the text box when uploading the ticket.

Make sure the patch was correctly uploaded by looking at it directly on the web page.

Set the ticket to needs review

You may ask somebody to review your ticket.

17. More on Mercurial queues

Other useful Mercurial commands when patches multiplies:

hg qnew
Create a new patch
hg qnew
...
hg qpop
Move a patch from the applied stack to the unapplied one
hg qpush
Move a patch from the unapplied stack to the applied one
hg qtop
Show the current patch
hg qseries
Print all of the patches in order

18. Dowload a patch

A feature available on a Sage Trac ticket interests you? You want to review a ticket?

Download a patch!

Insert a patch into the series after the last applied patch with hg qimport:

hg qimport ~/Downloads/trac_65321-nice-feature-AA.patch

Warning

Do NOT use the command hg import as it will import the changes in the current patch.

19. Edit the series file

You can change the order in which the patches are applied. To do so, simply edit the series file:

slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe $ cd .hg/patches/
slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe/.hg/patches $ vim series

Make sure the patch you are reviewing is the first patch to be applied:

slabbe@pol ~/Applications/sage-4.6.1/devel/sage-slabbe/.hg/patches $ cat series
trac_65321-nice-feature-AA.patch
A.patch
B.patch
C.patch

Warning

Patches might not commute, for example if they edit the exact same line.
If conflicts occur after editing the series file and doing hg qpush, simply edit the series file and try again.

20. Reviewing a patch

Visit the Reviewing a patch Section of the Sage Developer’s Guide. Also, make sure you read William Stein’s blog post about reviewing a Sage trac ticket.

Make sure the patch applies on Sage without conflicts:
hg qpush and hg qpop

Experiment the functionality proposed in the patch.

  • Make sure the bug described in the ticket is fixed.
  • Make sure the patch does not introduce any new bug.
Run tests on the affected files.
sage -t <affected_files>

20. Reviewing a patch

Test the entire Sage library.
sage --testall --long
Ensure that the documentation builds fine:
sage -docbuild reference html
Check for full 100% doctest coverage:
sage -coverage <file>

Once you’ve tested the patch, report any failures on the Trac page for the ticket. Make suggestions about simplifying the code or fixing typos you noticed.

21. Positive review or Needs work

Three cases may happen:

Needs work
Mark it as needs work if there is anything to do.
Positive review
Otherwise, mark it as positive review, and mention in a comment all the things you checked.
Delegate
If you don’t feel experienced enough for that, add a comment on the Trac page explaining what you have checked, what the results were, and that you think someone more experienced should take a look.

21. Positive review or Needs work

Note

In Sage, a negative review does not exist!
There is always place for work and improvement!

22. Do some cleaning

Delete an (unapplied) patch from the queue:

hg qdelete trac_65321-nice-feature-AA.patch

Erase your branch. Of course, do this only if you don’t care about your local changes:

rm -rf sage-slabbe

References

Sage

Sage trac

Sage Developer’s Guide

Reviewing a Sage trac ticket, William Stein’s blog post, October 31, 2010.

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